If the neck is not aligned properly it's either the wrong case or a bad batch. This is exactly what happened to me. I had to push it down in and the neck cutout was way off. I think it's the wrong case. I sent it back to PRS and they replaced it with the proper case. The neck lines up perfectly on the replacement case and it did not need to be pushed down in to fit properly. I've never had to push a PRS into the proper case. So send your case back and have PRS get you the right case.